A better track of contamination in ancient DNA

A new paper from Anja Furtwängler and coworkers finds that the usual way of estimating contamination fraction in ancient DNA samples may fall short: “Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis”.

The upshot is summarized in the abstract:

We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.

DNA from living or recently dead people can enter ancient samples at many different stages of recovery, conservation, and curation of remains. Some laboratory methods preferentially amplify modern DNA, which is a problem for researchers who want to reduce the cost of sequencing runs. So the cost-effectiveness of ancient DNA research depends upon finding ways to increase the fraction of endogenous DNA in sequencing runs.

Reducing costs is the main reason why ancient DNA labs have thrown so much effort into obtaining petrous bones. It is not a matter of better preservation so much as a matter of higher endogenous DNA content, which makes sequencing with today’s approaches relatively cheaper. The finding in this paper that petrosal samples have a more stable relation of mitochondrial and nuclear contamination rates will probably be cited as another point in favor of the predictability of petrosal versus other sampling approaches.